NAME

Bio::Phylo - Phylogenetic analysis using perl.

DESCRIPTION

This is the base class for the Bio::Phylo package. All other modules inherit from it, the methods defined here are applicable to all. Consult the manual for usage examples: Bio::Phylo::Manual.

METHODS

CONSTRUCTOR

new()

The Bio::Phylo object itself, and thus its constructor, is rarely, if ever, used directly. Rather, all other objects in this package inherit its methods, and call its constructor internally.

 Type    : Constructor
 Title   : new
 Usage   : my $phylo = Bio::Phylo->new;
 Function: Instantiates Bio::Phylo object
 Returns : a Bio::Phylo object
 Args    : -name    => (object name)
           -desc    => (object description)
           -score   => (numerical score)
           -generic => (generic key/value pair)

MUTATORS

set_name()
 Type    : Mutator
 Title   : set_name
 Usage   : $obj->set_name($name);
 Function: Assigns an object's name.
 Returns : Modified object.
 Args    : Argument must be a string,
           single quoted if it
           contains [;|,|:\(|\)]
set_desc()
 Type    : Mutator
 Title   : set_desc
 Usage   : $obj->set_desc($desc);
 Function: Assigns an object's description.
 Returns : Modified object.
 Args    : Argument must be a string.
set_score()
 Type    : Mutator
 Title   : set_score
 Usage   : $obj->set_score($score);
 Function: Assigns an object's numerical score.
 Returns : Modified object.
 Args    : Argument must be any of 
           perl's number formats.
set_generic()
 Type    : Mutator
 Title   : set_generic
 Usage   : $obj->set_generic(%generic);
 Function: Assigns generic key/value pairs to the invocant.
 Returns : Modified object.
 Args    : Valid arguments constitute 
           key/value pairs, for example:
           $node->set_generic(
               '-posterior' => 0.87565,
           );

ACCESSORS

get_name()
 Type    : Accessor
 Title   : get_name
 Usage   : my $name = $obj->get_name;
 Function: Returns the object's name (if any).
 Returns : A string
 Args    : None
get_desc()
 Type    : Accessor
 Title   : get_desc
 Usage   : my $desc = $obj->get_desc;
 Function: Returns the object's description (if any).
 Returns : A string
 Args    : None
get_score()
 Type    : Accessor
 Title   : get_score
 Usage   : my $score = $obj->get_score;
 Function: Returns the object's numerical score (if any).
 Returns : A number
 Args    : None
get_generic()
 Type    : Accessor
 Title   : get_generic
 Usage   : my $value = $obj->get_generic($key);
           or
           my %hash = %{ $obj->get_generic() };
 Function: Returns the object's generic data. If an
           argument is used, it is considered a key
           for which the associated value is return.
           Without arguments, a reference to the whole
           hash is returned.
 Returns : A string or hash reference.
 Args    : None
get_id()
 Type    : Accessor
 Title   : get_id
 Usage   : my $id = $obj->get_id;
 Function: Returns the object's unique ID
 Returns : INT
 Args    : None

PACKAGE METHODS

get()

All objects in the package subclass the Bio::Phylo object, and so, for example, you can do $node->get('get_branch_length'); instead of $node->get_branch_length. This is a useful feature for listable objects especially, as they have the get_by_value method, which allows you to retrieve, for instance, a list of nodes whose branch length exceeds a certain value. That method (and get_by_regular_expression) uses this $obj->get method.

 Type    : Accessor
 Title   : get
 Usage   : my $treename = $tree->get('get_name');
 Function: Alternative syntax for safely accessing 
           any of the object data; useful for 
           interpolating runtime $vars.
 Returns : (context dependent)
 Args    : a SCALAR variable, e.g. $var = 'get_name';
clone()
 Type    : Utility method
 Title   : clone
 Usage   : my $clone = $object->clone;
 Function: Creates a copy of the invocant object.
 Returns : A copy of the invocant.
 Args    : none.
VERBOSE()

Getter and setter for the verbose level. Currently it's just 0=no messages, 1=messages, but perhaps there could be more levels? For caller diagnostics and so on?

 Type    : Accessor
 Title   : VERBOSE(0|1)
 Usage   : Phylo->VERBOSE(0|1)
 Function: Sets/gets verbose level
 Returns : Verbose level
 Args    : 0=no messages; 1=error messages
 Comments:
CITATION()
 Type    : Accessor
 Title   : CITATION
 Usage   : $phylo->CITATION;
 Function: Returns suggested citation.
 Returns : Returns suggested citation.
 Args    : None
 Comments:
VERSION()
 Type    : Accessor
 Title   : VERSION
 Usage   : $phylo->VERSION;
 Function: Returns version number 
           (including CVS revision number).
 Alias   :
 Returns : SCALAR
 Args    : NONE
 Comments:
to_xml()
 Type    : Format converter
 Title   : to_cipres
 Usage   : my $xml = $obj->to_xml;
 Function: Turns the invocant object into an XML string.
 Returns : SCALAR
 Args    : NONE

DESTRUCTOR

DESTROY()
 Type    : Destructor
 Title   : DESTROY
 Usage   : $phylo->DESTROY
 Function: Destroys Phylo object
 Alias   :
 Returns : TRUE
 Args    : none
 Comments: You don't really need this, 
           it is called automatically when
           the object goes out of scope.

SEE ALSO

Also see the manual: Bio::Phylo::Manual.

FORUM

CPAN hosts a discussion forum for Bio::Phylo. If you have trouble using this module the discussion forum is a good place to start posting questions (NOT bug reports, see below): http://www.cpanforum.com/dist/Bio-Phylo

BUGS

Please report any bugs or feature requests to bug-bio-phylo@rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Phylo. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes. Be sure to include the following in your request or comment, so that I know what version you're using:

$Id: Phylo.pm,v 1.29 2006/04/12 22:38:22 rvosa Exp $

AUTHOR

Rutger Vos,

email: mailto://rvosa@sfu.ca
web page: http://www.sfu.ca/~rvosa/

ACKNOWLEDGEMENTS

The author would like to thank Jason Stajich for many ideas borrowed from BioPerl http://www.bioperl.org, and CIPRES http://www.phylo.org and FAB* http://www.sfu.ca/~fabstar for comments and requests.

COPYRIGHT & LICENSE

Copyright 2005 Rutger Vos, All Rights Reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.